Depiction
- Various ways to depict biological networks:
- Node-Link (graph) representation
- Partitioned Node-Link representation
- Matrix representation
- Can be useful for very dense networks
- Can also map information into cells of matrix
- e.g. degree, color scale (heat map)
Data Mapping
- Mapping of data values associated with graph elements onto graph visuals
- Visual attributes
- Node fill color, border color, border width, size, shape, opacity, label
- Edge type, color, width, ending type, ending size, ending color
- Mapping types
- Continuous (numeric values)
- Discrete (categories)
- Passthrough (labels)
Data Mapping
- Avoid cluttering your visualization with too much data
- Highlight meaningful differences
- Avoid confusing the viewer
- Consider creating multiple network images
Layouts
- Layouts determine the location of nodes and (sometimes) the paths of edges
- Types:
- Simple
- Hierarchical
- layout data as a tree or hierarchy
- Works best when there are no loops
- Circular (Radial)
- arrange nodes around a circle
- could use node attributes to govern position
Layouts
- Types:
- Force-Directed
- simulate edges as springs
- may be weighted or unweighted
- Combining layouts
- Use a general layout (force directed) for the entire graph,
but use hierarchical or radial to focus on a particular portion
- Multi-layer layouts
- Partition graph, layout each partition then layout partitions
- Many, many others
Layouts
- Manual tweaks with Node Layout Tools
Menu: Layout > Node Layout Tools
Layouts
- Use layouts to convey the relationships between the nodes.
- There is not one correct layout. Try different things.
- Layout algorithms may need to be “tuned” to fit your network.
Animation
- Animation is useful to show changes in a network:
- Over a time series
- Over different conditions
- Between species
